Well I successfully got two (I’m fairly certain that it will work for more) identical canon scanners hooked to the system with twain. It’s clear that it’s not really a limitation of twain. It took some registry hacking to get things going. I can even change the names that show up in the twain source selection to name each scanner according to its location.
The key to keeping things straight is to setup each scanner one at a time. First plug one in to a usb port and windows will auto install it into the system. Then I rename/reconfigure the canon registry info. (This holds the datasource name and what directory the datasource is in. It also holds what usb port the scanner is hooked to.) and rename the datasource directory in windowstwain_32. Then when I plug another scanner into another usb port and windows auto installs it the other scanner(s) setup doesn’t get overwritten, then repeat the process. Surprisingly simple. It’s pretty cool to see it work so well. I only wish that there was a more standard, abstracted way of doing this that would work with any brand/model of scanner.